About GLUE
- Who develops GLUE?
- What license does GLUE have?
- How can I get the source code for GLUE?
- How can I cite GLUE?
- What software does GLUE itself use?
GLUE is developed by the Gifford Lab.
GLUE is free, open source software, and you are welcome to use, modify and redistribute it under certain conditions set out in its license. GLUE is licensed under the GNU Affero General Public License version 3.0.
The source code is available on GitHub: https://github.com/giffordlabcvr/gluetools.
NOTE: The vast majority of GLUE users probably do not need to build GLUE from source, and should install the binary distribution.
You can find detailed instructions on how to install GLUE from its binary distribution here: http://glue-tools.cvr.gla.ac.uk/#/installation.
There is a journal article on the GLUE software system generally:
GLUE: A flexible software system for virus sequence data
Joshua B Singer, Emma C Thomson, John McLauchlan, Joseph Hughes and Robert J Gifford
BMC Bioinformatics 2018 19:532
https://doi.org/10.1186/s12859-018-2459-9
In addition there is an article focusing on the GLUE features for analysing deep sequencing data:
Interpreting Viral Deep Sequencing Data with GLUE
Joshua B Singer, Emma C Thomson, Joseph Hughes, Elihu Aranday-Cortes, John McLauchlan, Ana da Silva Filipe, Lily Tong, Carmen F Manso, Robert J Gifford, David L Robertson, Eleanor Barnes, M. Azim Ansari, Jean L Mbisa, David F Bibby, Daniel Bradshaw and David Smith
Viruses 2019 11(4), 323
https://doi.org/10.3390/v11040323
GLUE uses many different pieces of software provided by other groups. The "Runtime dependencies" are software pieces which you must install yourself before running GLUE. Other items are bundled with the GLUE engine.
| Software | Version | Dependency type | Web link |
|---|---|---|---|
| Java Platform Standard Edition | 1.8.0 | Runtime dependency of GLUE | https://www.oracle.com/java/technologies/java-se.html |
| MySQL Server Community Edition | 5.7+ | Runtime dependency of GLUE | https://www.mysql.com/ |
| BLAST+ | 2.2.31 | Runtime dependency of GLUE | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| MAFFT | 7.299b | Runtime dependency of GLUE | https://mafft.cbrc.jp/alignment/software/ |
| RAxML | 8.2.8 | Runtime dependency of GLUE | https://sco.h-its.org/exelixis/web/software/raxml/index.html |
| underscore.js | 1.8.3 | JavaScript library, bundled with GLUE engine | http://underscorejs.org/ |
| Apache HttpComponents | 4.4.1 | Java library, bundled with GLUE engine | https://hc.apache.org/ |
| Apache Cayenne | 3.1.1 | Java library, bundled with GLUE engine | https://cayenne.apache.org/ |
| Apache Commons IO | 1.3.2 | Java library, bundled with GLUE engine | https://commons.apache.org/proper/commons-io/ |
| Apache FreeMarker | 2.3.25 | Java library, bundled with GLUE engine | https://freemarker.apache.org/ |
| Apache Commons Collections | 3.2 | Java library, bundled with GLUE engine | https://commons.apache.org/proper/commons-collections/ |
| MySQL Connector / Java | 8.0.13 | Java library, bundled with GLUE engine | https://dev.mysql.com/downloads/connector/j/ |
| JLine2 | 2.14.5 | Java library, bundled with GLUE engine | https://github.com/jline/jline2 |
| data-exporter | 1.0.4 | Java library, bundled with GLUE engine | https://github.com/brsanthu/data-exporter |
| docopt.java | 0.6.0.20150202 | Java library, bundled with GLUE engine | https://github.com/docopt/docopt.java |
| GlassFish JSON implementation | 1.0.4 | Java library, bundled with GLUE engine | https://javaee.github.io/glassfish/ |
| SAMtools HTSJDK | 2.0.1 | Java library, bundled with GLUE engine | https://github.com/samtools/htsjdk |
| Trove4J | 3.0.3 | Java library, bundled with GLUE engine | https://bitbucket.org/trove4j/trove |
| Apache Commons Lang | 3.0 | Java library, bundled with GLUE engine | https://commons.apache.org/proper/commons-lang/ |
| Apache Commons BCEL | 6.0 | Java library, bundled with GLUE engine | https://commons.apache.org/proper/commons-bcel/ |
| GlassFish Jersey | 2.19 | Java library, bundled with GLUE web services engine | https://jersey.github.io/ |
GLUE by Robert J. Gifford Lab.
For questions, issues, or feedback, please open an issue on the GitHub repository.